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Job request: 1977

Organisation:
Bennett Institute
Workspace:
faw_vaccine
ID:
hpom2fk3gdm3ny5d
View repo View project.yaml

This page shows the technical details of what happened when authorised researcher Millie Green requested one or more actions to be run against real patient data in the project, within a secure environment.

By cross-referencing the indicated Requested Actions with the Pipeline section below, you can infer what security level various outputs were written to. Outputs marked as highly_sensitive can never be viewed directly by a researcher; they can only request that code runs against them. Outputs marked as moderately_sensitive can be viewed by an approved researcher by logging into a highly secure environment. Only outputs marked as moderately_sensitive can be requested for release to the public, via a controlled output review service.

Jobs

Pipeline

Show project.yaml 
######################################

# This script defines the project pipeline - it specifys the execution orders for all the code in this
# repo using a series of actions.

######################################

version: '3.0'

expectations:
  population_size: 1000000

actions:

  # Extract data for study population flow chart
  generate_study_population_flow_chart_data:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_flow_chart
    outputs:
      highly_sensitive:
        cohort: output/input_flow_chart.csv

  # Calculate numbers for study population flow chart
  flow_chart:
    run: r:latest -e 'rmarkdown::render("analysis/R/Markdown/Study_definition_flow_chart.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
    needs: [generate_study_population_flow_chart_data]
    outputs:
      moderately_sensitive:
        html: output/Study_definition_flow_chart.html
        
  # Extract study data
  generate_study_population:
    run: cohortextractor:latest generate_cohort --study-definition study_definition
    outputs:
      highly_sensitive:
        cohort: output/input.csv
        
  # Process data
  data_process:
    run: r:latest analysis/R/Scripts/00_process_data.R
    needs: [generate_study_population]
    outputs:
      highly_sensitive:
        data1: output/data/data_all.rds
        data2: output/data/data_modelling.rds
        
  # Summarise data
  data_properties:
    run: r:latest analysis/R/Scripts/01_data_properties.R output/data/data_all.rds output/data_properties
    needs: [generate_study_population, data_process]
    outputs:
      moderately_sensitive:
        datasummary: output/data_properties/data_all*.txt
        
  # More data summaries
  data_summaries:
    run: r:latest -e 'rmarkdown::render("analysis/R/Markdown/Data_summaries.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
    needs: [generate_study_population, data_process]
    outputs:
      moderately_sensitive:
        html: output/Data_summaries.html

  # # Coxph models
  # cox_models:
  #   run: r:latest analysis/R/Scripts/02a_models_coxph.R
  #   needs: [generate_study_population, data_process]
  #   outputs:
  #     highly_sensitive :
  #       models: output/models/testing/mod*.rds
        
  # # Coxme model
  # coxme_model:
  #   run: r:latest analysis/R/Scripts/02b_models_coxme.R
  #   needs: [generate_study_population, data_process]
  #   outputs:
  #     highly_sensitive :
  #       models: output/models/testing/mod_test*.rds
  
  # # Model summaries
  # cox_models_summaries:
  #   run: r:latest -e 'rmarkdown::render("analysis/R/Markdown/Model_comparisons.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
  #   needs: [generate_study_population, data_process, cox_models, coxme_model]
  #   outputs:
  #     moderately_sensitive:
  #       html: output/Model_comparisons.html
  
  # AFT vs Cox models feasibility
  aft_vs_cox_poc:
    run: r:latest analysis/R/Scripts/02c_models_cox_vs_aft_poc.R
    needs: [generate_study_population, data_process]
    outputs:
      highly_sensitive :
        models: output/models/testing/cox_vs_aft/mod*.rds
      moderately_sensitive:
        tables: output/models/testing/cox_vs_aft/table*.csv
        plots: output/models/testing/cox_vs_aft/plot*.svg

  # AFT models
  aft_vs_cox_models:
    run: r:latest analysis/R/Scripts/02d_models_cox_vs_aft.R
    needs: [generate_study_population, data_process]
    outputs:
      highly_sensitive :
        models: output/models/cox_vs_aft/mod*.rds
        
  # Model comparison
  aft_vs_cox_comparison:
    run: r:latest -e 'rmarkdown::render("analysis/R/Markdown/Cox_vs_aft_model_comparison.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
    needs: [generate_study_population, data_process, aft_vs_cox_models]
    outputs:
      moderately_sensitive:
        html: output/Cox_vs_aft_model_comparison.html
        
  # # Final (AFT) model
  # model_final:
  #   run: r:latest analysis/R/Scripts/03_Final_model.R
  #   needs: [generate_study_population, data_process]
  #   outputs:
  #     highly_sensitive :
  #       models: output/models/final/mod*.rds
      # moderately_sensitive:
      #   tables: output/models/final/tab*.html
      #   data: output/models/final/tab*.csv
      #   plots: output/models/final/plot*.svg
 
  # # Strata summaries
  # strata_summary:
  #   run: r:latest analysis/R/Scripts/04_Strata_Summary.R
  #   needs: [data_process, model_final]
  #   outputs:
  #     moderately_sensitive:
  #       plots: output/models/final/plot_strata*.svg
  
  # # Results summary
  # results_summary:
  #   run: r:latest -e 'rmarkdown::render("analysis/R/Markdown/Results_summary.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
  #   needs: [generate_study_population, data_process, model_final]
  #   outputs:
  #     moderately_sensitive:
  #       html: output/Results_summary.html

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 01:36:36

These timestamps are generated and stored using the UTC timezone on the TPP backend.

Job information

Status
Succeeded
Backend
TPP
Workspace
faw_vaccine
Requested by
Millie Green
Branch
AFT
Force run dependencies
No
Git commit hash
f5b97c8
Requested actions
  • aft_vs_cox_models

Code comparison

Compare the code used in this Job Request